User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.3k
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Italy
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@jotsetung
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Joined:
3 years, 9 months ago
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j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 240 results • page 1 of 24 • next >
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Comment: C: XCMS for GC-MS
... I don't have any GC-MS data examples, but I guess the processing is pretty much the same as for LC-MS, so you can use xcms for the processing. Have a look at the xcms vignettes for examples on the preprocessing. Eventually you could also have a look at https://github.com/jotsetung/metabolomics2018 t ...
written 11 days ago by Johannes Rainer1.3k
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Comment: C: Chromatographic peak detection failed for all files
... 1st, please re-install mzR using BiocInstaller::biocLite("mzR"). For the error, seems that proteowizard has problems reading this file. Can you please try the second part, i.e. with openMSfile and the backend = "Ramp" option? ...
written 7 weeks ago by Johannes Rainer1.3k
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Comment: C: Chromatographic peak detection failed for all files
... From the error message I'd say there is a problem in reading your files. Some time ago we switched from mzML/mzXML data import using the Ramp backend to the proteowizard libraries (because they represent the standard implementation of the mzML format). Could you please try the following: library( ...
written 7 weeks ago by Johannes Rainer1.3k
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Comment: C: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
... Just one more note on the EnsDb databases/packages. The package Aaron was using above is based on Ensembl release 86. You should make sure to use annotations from the same Ensembl release throughout your analysis. While the release 86 EnsDb is the most recent one provided as annotation package, you ...
written 8 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I guess so. I've never done that but it should work. ...
written 10 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I just checked the tx IDs in the ncrna and the cdna files and they are not overlapping. So both files contain a different set of genes/transcripts. ...
written 10 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I would assume that most (if not all) ncRNAs are in the ncrna fasta file (e.g. homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz). I've checked and all of the IDs in this file are present in the EnsDb (for Ensembl version 92). ...
written 10 weeks ago by Johannes Rainer1.3k
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Answer: A: Create Ensembl transcript to gene IDs table with R ensembldb package for tximpor
... Re question 1: To get an overview of all available EnsDb databases for mouse you use AnnotationHub, not ensembldb: > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2018-04-30 > query(ah, "EnsDb.Mmusculus") AnnotationHub with 6 records # snapshotDate(): 2018-04-30 # $da ...
written 12 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Both the EnsDb from the link above and the cdna fasta file are based on Ensembl release 92, so all transcripts from the cdna fasta file should be in the EnsDb. Note however that transcript IDs in EnsDb databases are without the transcript version (e.g. the ".1" in "ENST00001.1"). Did you use ignoreT ...
written 3 months ago by Johannes Rainer1.3k
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Answer: A: Metabolite identification package
... I guess you have already identified the chromatographic peaks/features with xcms, what you could do then is to use the CAMERA package to find adducts and isotopes in your data. Ultimately you will however have to look up the m/z of your peaks in a database (like hmdb (https://hmdb.ca)) to find possi ...
written 3 months ago by Johannes Rainer1.3k

Latest awards to Johannes Rainer

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Appreciated 13 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 13 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 13 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 13 months ago, received more than 100 upvotes.
Voter 13 months ago, voted more than 100 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Appreciated 13 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 13 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 13 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 13 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 14 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 14 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 15 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 16 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Scholar 16 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.3 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Scholar 2.3 years ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 2.3 years ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.3 years ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74

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